We are looking at an influenza virus hemaglutinin peptide 306-318
sitting in the groove (magenta) of a human class II MHC molecule
(HLA-DR1). We are looking at the face to which the T cell antigen
receptor would bind. Most of the 13 amino acid peptide's side chains
interact with the lips and floor (yellow) of the groove, but several
stick up forming the T cell determinant for this peptide. Compare
with the sendai and VSV peptides in MHC class I grooves. Notice
that the ends of the longer peptide here protrude out of the ends of
The peptide uses RasMol's Corey/Pauling/Koltun color scheme: carbon
is gray, oxygen is red, and nitrogen is blue. Hydrogens would be white
but are not resoved by X-ray crystallography.
This image was constructed from images in a
RasMol "movie" script.
The atomic coordinate file employed is
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